7WKM

Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol

• PDB DOI: https://doi.org/10.2210/pdb7WKM/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-10 Released: 2023-01-25 
• Deposition Author(s): Fan, Y., Xue, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.177 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 

Starting Model: experimental

Literature

The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase

Fan, Y., Wu, S., Shi, J., Li, X., Yang, Y., Feng, Y., Xue, S.

(2023) Appl Microbiol Biotechnol 107: 7451-7462

• DOI: https://doi.org/10.1007/s00253-023-12813-9

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 78.36 kDa 
• Atom Count: 6,322 
• Modelled Residue Count: 678 
• Deposited Residue Count: 678 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A, B	339	Aspergillus oryzae	Mutation(s): 0  EC: 4.1.1.46
UniProt
Find proteins for P80402 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P80402  Go to UniProtKB:  P80402

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAQ (Subject of Investigation/LOI)	D [auth A], F [auth B]	CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.177 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.415	α = 90
b = 99.415	β = 90
c = 128.921	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Fan, Y., Xue, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877110

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-01-03
  Changes: Database references, Structure summary